The three stages in CRISPR-Cas system are CRISPR spacer integration, CRISPR expression and Interference.

• CRISPR spacer integration: The foreign DNA segments, referred to as protospacer, are recognized and integrated between two adjacent repeats in the CRISPR locus region, forming the CRISPR array. The protospacer adjacent motif (PAM), a short stretch of conserved nucleotides exists in proximal to the protospacer, is serving as the recognition motif for acquiring the DNA fragment.
• CRISPR expression: CRISPR arrays are transcribed by RNA polymerase into pre-crRNA (precursor CRISPR RNA), which are further cleaved by Cas proteins into small crRNAs. The crRNA contains a partial repeat and a single spacer that is derived from and complementary to a fragment of the foreign DNA.
• Interference: Cas proteins bind to the crRNA- foreign DNA complex and cleave the DNA segment. DNA cleavage interferes with viral replication and provides immunity to the host cell.